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NM_000236.3(LIPC):c.674G>A (p.Arg225Gln) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 26, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003336506.1

Allele description [Variation Report for NM_000236.3(LIPC):c.674G>A (p.Arg225Gln)]

NM_000236.3(LIPC):c.674G>A (p.Arg225Gln)

Gene:
LIPC:lipase C, hepatic type [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
15q21.3
Genomic location:
Preferred name:
NM_000236.3(LIPC):c.674G>A (p.Arg225Gln)
HGVS:
  • NC_000015.10:g.58545841G>A
  • NG_011465.2:g.118866G>A
  • NM_000236.3:c.674G>AMANE SELECT
  • NP_000227.2:p.Arg225Gln
  • NC_000015.9:g.58838040G>A
  • NM_000236.2:c.674G>A
Protein change:
R225Q
Links:
dbSNP: rs575306493
NCBI 1000 Genomes Browser:
rs575306493
Molecular consequence:
  • NM_000236.3:c.674G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Type 2 diabetes mellitus
Synonyms:
DIABETES MELLITUS, TYPE 2, PROTECTION AGAINST; Type II diabetes mellitus; Diabetes mellitus, noninsulin-dependent, late onset
Identifiers:
MONDO: MONDO:0005148; MeSH: D003924; MedGen: C0011860; OMIM: 125853; Human Phenotype Ontology: HP:0005978
Name:
High density lipoprotein cholesterol level quantitative trait locus 12 (HDLCQ12)
Identifiers:
MedGen: C2675071; OMIM: 612797
Name:
Hyperlipidemia due to hepatic triglyceride lipase deficiency
Synonyms:
LIPC DEFICIENCY; Hepatic lipase deficiency
Identifiers:
MONDO: MONDO:0013533; MedGen: C3151466; OMIM: 614025

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004046498New York Genome Center
criteria provided, single submitter

(NYGC Assertion Criteria 2020)		Uncertain significance
(Jan 26, 2023) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot provided1not providedclinical testing

Details of each submission

From New York Genome Center, SCV004046498.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The c.674G>A variant in LIPC has not previously been reported in individuals with Hepatic lipase deficiency or non-insulin dependent diabetes mellitus; it has been deposited in ClinVar [ClinVar ID: 1678437] as variant of uncertain significance. The c.674G>A variant is observed in 57 alleles (~0.01% minor allele frequency with 0 homozygotes) in population databases (gnomAD v2.1.1 and v3.1.2, TOPMed Freeze 8), suggesting it is not a common benign variant in the populations represented in those databases. The c.674G>A variant in LIPC is located in exon 5 of this 9-exon gene, and is predicted to replace an evolutionarily not-highly-conserved arginine amino acid with glutamine at position 225 (p.(Arg225Gln)) in a nonspecific region of the encoded protein. In silico predictions are not in favor of damaging effect for the p.(Arg225Gln) variant [CADD v1.6 = 11.39, REVEL = 0.157]; however, there are no functional studies to support or refute these predictions. Based on available evidence this c.674G>A p.(Arg225Gln) variant identified in LIPC is classified as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown1not providednot provided1not providednot providednot provided

Last Updated: Sep 16, 2024